pseudotime.tree

This function takes an object of class iCellR and marker genes for clusters and performs pseudotime for differentiation or time course analysis.

A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.

Alireza Khodadadi-Jamayran

iCellR

Analyzing High-Throughput Single Cell Sequencing Data

Joseph Pucella

Hua Zhou

Nicole Doudican

John Carucci

Adriana Heguy

Boris Reizis

Aristotelis Tsirigos

pseudotime.tree function

<dl><dt>x</dt>
<dd>An object of class iCellR.</dd>
<dt>marker.genes</dt>
<dd>A list of marker genes for clusters.</dd>
<dt>clust.names</dt>
<dd>A list of names for clusters.</dd>
<dt>dist.method</dt>
<dd>Choose from "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski", default = "euclidean".</dd>
<dt>clust.method</dt>
<dd>Choose from "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid", default = "complete".</dd>
<dt>label.offset</dt>
<dd>Space between names and tree, default = 0.5.</dd>
<dt>type</dt>
<dd>Choose from "classic", "jitter", "unrooted", "fan", "cladogram", "radial", default = "classic".</dd>
<dt>hang</dt>
<dd>Hang, default = 1.</dd>
<dt>cex</dt>
<dd>Text size, default = 1.</dd></dl>

Arguments

Pseudotime Tree — pseudotime.tree

<dl>

<dt>x</dt>
<dd>An object of class iCellR.</dd>


<dt>marker.genes</dt>
<dd>A list of marker genes for clusters.</dd>


<dt>clust.names</dt>
<dd>A list of names for clusters.</dd>


<dt>dist.method</dt>
<dd>Choose from "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski", default = "euclidean".</dd>


<dt>clust.method</dt>
<dd>Choose from "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid", default = "complete".</dd>


<dt>label.offset</dt>
<dd>Space between names and tree, default = 0.5.</dd>


<dt>type</dt>
<dd>Choose from "classic", "jitter", "unrooted", "fan", "cladogram", "radial", default = "classic".</dd>


<dt>hang</dt>
<dd>Hang, default = 1.</dd>


<dt>cex</dt>
<dd>Text size, default = 1.</dd>

</dl>

pseudotime.tree: Pseudotime Tree

Description

Usage

Value

Arguments